Identification of maize long non-coding RNAs responsive to drought stress.

Zhang W, Han Z, Guo Q, Liu Y, Zheng Y, Wu F, Jin W - PLoS ONE (2014)

Bottom Line:
The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules.Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress.These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.

Affiliation: College of Life Sciences, Northwest A&F University, Yangling, China.

ABSTRACTLong non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed to shorter miRNAs and siRNAs. Emerging evidence shows that lncRNAs participate in stress responsive regulation. In this study, to identify the putative maize lncRNAs responsive to drought stress, 8449 drought responsive transcripts were first uploaded to the Coding Potential Calculator website for classification as protein coding or non-coding RNAs, and 1724 RNAs were identified as potential non-coding RNAs. A Perl script was written to screen these 1724 ncRNAs and 664 transcripts were ultimately identified as drought-responsive lncRNAs. Of these 664 transcripts, 126 drought-responsive lncRNAs were highly similar to known maize lncRNAs; the remaining 538 transcripts were considered as novel lncRNAs. Among the 664 lncRNAs identified as drought responsive, 567 were upregulated and 97 were downregulated in drought-stressed leaves of maize. 8 lncRNAs were identified as miRNA precursor lncRNAs, 62 were classified as both shRNA and siRNA precursors, and 279 were classified as siRNA precursors. The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules. Among these 315 lncRNAs, 10 are identified as antisense lncRNAs and 7 could pair with 17 CDS sequences with near-perfect matches. Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress. These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.

pone-0098958-g003: The TCONS_00012703 were mapped with multiple siRNA reads.

Mentions:
Based on the established mechanisms of biogenesis, siRNAs are expected to derive from a longer molecule cleaved into multiple sRNAs through specific endonuclease activity. To determine if multiple sRNAs are derived from siRNA precursor ncRNAs, 341 siRNA precursor ncRNAs were mapped to siRNA reads and subjected to further analysis. Results show that most of the siRNA precursor lncRNAs produced more than one sRNA (Table S5). For instance, Figure 3 shows that TCONS_00012703 is homologous to multiple siRNA reads. In addition, the RT-qPCR result of TCONS_00012703 RNA demonstrates that the expression level of the lncRNAs is relatively low in both non-stressed leaves and roots but accumulates to high levels after drought stress in both plant tissues (Figure 4A).

pone-0098958-g003: The TCONS_00012703 were mapped with multiple siRNA reads.

Mentions:
Based on the established mechanisms of biogenesis, siRNAs are expected to derive from a longer molecule cleaved into multiple sRNAs through specific endonuclease activity. To determine if multiple sRNAs are derived from siRNA precursor ncRNAs, 341 siRNA precursor ncRNAs were mapped to siRNA reads and subjected to further analysis. Results show that most of the siRNA precursor lncRNAs produced more than one sRNA (Table S5). For instance, Figure 3 shows that TCONS_00012703 is homologous to multiple siRNA reads. In addition, the RT-qPCR result of TCONS_00012703 RNA demonstrates that the expression level of the lncRNAs is relatively low in both non-stressed leaves and roots but accumulates to high levels after drought stress in both plant tissues (Figure 4A).

Bottom Line:
The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules.Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress.These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.

Affiliation:
College of Life Sciences, Northwest A&F University, Yangling, China.

ABSTRACTLong non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed to shorter miRNAs and siRNAs. Emerging evidence shows that lncRNAs participate in stress responsive regulation. In this study, to identify the putative maize lncRNAs responsive to drought stress, 8449 drought responsive transcripts were first uploaded to the Coding Potential Calculator website for classification as protein coding or non-coding RNAs, and 1724 RNAs were identified as potential non-coding RNAs. A Perl script was written to screen these 1724 ncRNAs and 664 transcripts were ultimately identified as drought-responsive lncRNAs. Of these 664 transcripts, 126 drought-responsive lncRNAs were highly similar to known maize lncRNAs; the remaining 538 transcripts were considered as novel lncRNAs. Among the 664 lncRNAs identified as drought responsive, 567 were upregulated and 97 were downregulated in drought-stressed leaves of maize. 8 lncRNAs were identified as miRNA precursor lncRNAs, 62 were classified as both shRNA and siRNA precursors, and 279 were classified as siRNA precursors. The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules. Among these 315 lncRNAs, 10 are identified as antisense lncRNAs and 7 could pair with 17 CDS sequences with near-perfect matches. Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress. These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.